passing multiple arguments to a python function from bash (in variables)

Question

I wrote a python function called plot_ts_ex that takes two arguments ts_file and ex_file (and the file name for this function is pism_plot_routine). I want to run this function from a bash script from terminal. When I don't use variables in the bash script in pass the function arguments (in this case ts_file = ts_g10km_10ka_hy.nc and ex_file = ex_g10km_10ka_hy.nc) directly, like this:

#!/bin/sh
python -c 'import pism_plot_routine; pism_plot_routine.plot_ts_ex("ts_g10km_10ka_hy.nc", "ex_g10km_10ka_hy.nc")'

which is similar as in Run function from the command line, that works.

But when I define variables for the input arguments, it doesn't work:

#!/bin/sh 
ts_name="ts_g10km_10ka_hy.nc" 
ex_name="ex_g10km_10ka_hy.nc" 
python -c 'import pism_plot_routine; pism_plot_routine.plot_ts_ex("$ts_name", "$ex_name")'

It gives the error:

FileNotFoundError: [Errno 2] No such file or directory: b'$ts_name'

Then I found a similar question passing an argument to a python function from bash for a python function with only one argument and I tried

#!/bin/sh
python -c 'import sys, pism_plot_routine; pism_plot_routine.plot_ts_ex(sys.argv[1])' "$ts_name" "$ex_name"

but that doesn't work.

So how can I pass 2 arguments for a python function in a bash script using variables?

Cubix48 · Accepted Answer · 2022-02-25 13:03:37Z

3

When you use single quotes the variables aren’t going to be expanded, you should use double quotes instead:

#!/bin/sh 
ts_name="ts_g10km_10ka_hy.nc" 
ex_name="ex_g10km_10ka_hy.nc" 
python -c "import pism_plot_routine; pism_plot_routine.plot_ts_ex('$ts_name', '$ex_name')"

You can also use sys.argv, arguments are stored in a list, so ts_name is sys.arv[1] and ex_name is sys.argv[2]:

#!/bin/sh 
ts_name="ts_g10km_10ka_hy.nc" 
ex_name="ex_g10km_10ka_hy.nc" 
python -c 'import sys, pism_plot_routine; pism_plot_routine.plot_ts_ex(sys.argv[1], sys.argv[2])' "$ts_name" "$ex_name"

answered Feb 25, 2022 at 13:03

Cubix48

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Riqk · Accepted Answer · 2022-02-25 13:01:50Z

2

You are giving the value $ts_name to python as string, bash does not do anything with it. You need to close the ', so that it becomes a string in bash, and then open it again for it to become a string in python.

The result will be something like this:

#!/bin/sh 
ts_name="ts_g10km_10ka_hy.nc" 
ex_name="ex_g10km_10ka_hy.nc" 
python -c 'import pism_plot_routine; pism_plot_routine.plot_ts_ex("'$ts_name'", "'$ex_name'")'

For issues like this it is often nice to use some smaller code to test it, I used python3 -c 'print("${test}")' to figure out what it was passing to python, without the bother of the pism_plot.

answered Feb 25, 2022 at 13:01

Riqk

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